Updated: Thu Dec 18 09:57:30 2014

DMR identification with methyl_diff

Background


UMR summary and sanity check

Sample Total.DMR Hyper.DMR Hypo.DMR
Cortex-HuFNSC02_Cortex-HuFNSC04 1283 179 1104
GE-HuFNSC02_GE-HuFNSC04 3002 722 2280

UMR asymmetry

GREAT enrichment for GW-associated UMRs

UMR Genomic breakdown

Proximal UMRs and DE genes

proximal.DMRs unique.genes DE.DMRs unique.DE.genes same.direction
Cortex04.UMRs 7 7 0 0 0
Cortex02.UMRs 215 215 24 19 21
GE04.UMRs 37 36 6 5 3
GE02.UMRs 402 402 64 57 49

Proximal 13-week UMRs in both Cortex and GE

id name description
ENSG00000189334 S100A14 S100_calcium_binding_protein_A14_[Source:HGNC_Symbol;Acc:18901]
ENSG00000237693 IRGM immunity-related_GTPase_family,M[Source:HGNC_Symbol;Acc:29597]
ENSG00000124564 SLC17A3 solute_carrier_family_17_(sodium_phosphate),member3_[Source:HGNC_Symbol;Acc:10931]

Proximal GE 13-week UMRs with DE genes

id name description DM DE
ENSG00000134954 ETS1 v-ets_erythroblastosis_virus_E26_oncogene_homolog_1_(avian)_[Source:HGNC_Symbol;Acc:3488] hyper UP
ENSG00000136352 NKX2-1 NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825] hyper UP
ENSG00000165588 OTX2 orthodenticle_homeobox_2_[Source:HGNC_Symbol;Acc:8522] hyper UP
ENSG00000231421 hyper DN
ENSG00000155760 FZD7 frizzled_family_receptor_7_[Source:HGNC_Symbol;Acc:4045] hyper DN

Proximal 17-week UMRs with DE genes in both Cortex and GE

id name description DM DE
ENSG00000255737 NA HCG2014417,isoformCRA_aUncharacterized_proteincDNA_FLJ59598_[Source:UniProtKB/TrEMBL;Acc:B7Z718] hypo UP
ENSG00000167178 ISLR2 immunoglobulin_superfamily_containing_leucine-rich_repeat_2_[Source:HGNC_Symbol;Acc:29286] hypo UP
ENSG00000161999 JMJD8 jumonji_domain_containing_8_[Source:HGNC_Symbol;Acc:14148] hypo UP
ENSG00000051523 CYBA cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577] hypo UP
ENSG00000169515 CCDC8 coiled-coil_domain_containing_8_[Source:HGNC_Symbol;Acc:25367] hypo UP
ENSG00000205927 OLIG2 oligodendrocyte_lineage_transcription_factor_2_[Source:HGNC_Symbol;Acc:9398] hypo UP
ENSG00000189060 H1F0 H1_histone_family,member0_[Source:HGNC_Symbol;Acc:4714] hypo UP
ENSG00000146904 EPHA1 EPH_receptor_A1_[Source:HGNC_Symbol;Acc:3385] hypo UP
ENSG00000165072 MAMDC2 MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673] hypo UP

UMRs overlapping with TFBS

TF UMR17week_Cortex UMR13week_Cortex Ratio_Cortex UMR17week_GE UMR13week_GE Ratio_GE
MAZ 133 5 26.6000 319 12 26.5833
GTF2F1 28 1 28.0000 103 2 51.5000
ZBTB7A 97 3 32.3333 201 3 67.0000
HMGN3 66 2 33.0000 131 4 32.7500
NRF1 34 1 34.0000 64 1 64.0000
MXI1 112 3 37.3333 262 7 37.4286
E2F4 50 1 50.0000 110 1 110.0000
CCNT2 87 1 87.0000 148 4 37.0000
E2F6 140 1 140.0000 263 8 32.8750

UMR enrichment at chromosome ends

DE genes summary

UP DN DE GW
cortex01_cortex03 284 281 565 17 vs 15
cortex01_cortex04 365 165 530 17 vs 13
cortex02_cortex03 398 283 681 17 vs 15
cortex02_cortex04 497 225 722 17 vs 13
cortex03_cortex04 459 183 642 15 vs 13
GE01_GE03 587 274 861 17 vs 15
GE01_GE04 645 238 883 17 vs 13
GE02_GE03 609 312 921 17 vs 15
GE02_GE04 610 259 869 17 vs 13
GE03_GE04 313 232 545 15 vs 13

Stage-specific DE gene profiles

  1. GW13-15:UP, GW15-17:UP;
    No genes
  2. GW13-15:UP, GW15-17:DN;
    id name description
    ENSG00000168542 COL3A1 collagen,typeIII,alpha1_[Source:HGNC_Symbol;Acc:2201]
    ENSG00000133636 NTS neurotensin_[Source:HGNC_Symbol;Acc:8038]
    ENSG00000066032 CTNNA2 catenin_(cadherin-associated_protein),alpha2_[Source:HGNC_Symbol;Acc:2510]
    ENSG00000135063 FAM189A2 family_with_sequence_similarity_189,memberA2_[Source:HGNC_Symbol;Acc:24820]
    ENSG00000214401
    ENSG00000099984 GSTT2 glutathione_S-transferase_theta_2_[Source:HGNC_Symbol;Acc:4642]
    ENSG00000238083 LRRC37A2 leucine_rich_repeat_containing_37,memberA2_[Source:HGNC_Symbol;Acc:32404]
    ENSG00000101255 TRIB3 tribbles_homolog_3_(Drosophila)_[Source:HGNC_Symbol;Acc:16228]
    ENSG00000160284 C21orf56 chromosome_21_open_reading_frame_56_[Source:HGNC_Symbol;Acc:1298]
  3. GW13-15:DN, GW15-17:UP;
    id name description
    ENSG00000022556 NLRP2 NLR_family,pyrindomain_containing_2_[Source:HGNC_Symbol;Acc:22948]
    ENSG00000225607 NA Uncharacterized_proteincDNA_FLJ60024,highlysimilar_to_Cytochrome_P450_4F12__[Source:UniProtKB/TrEMBL;Acc:B4DNA9]
    ENSG00000147813 NAPRT1 nicotinate_phosphoribosyltransferase_domain_containing_1_[Source:HGNC_Symbol;Acc:30450]
    ENSG00000167654 ATCAY ataxia,cerebellar,Cayman_type_[Source:HGNC_Symbol;Acc:779]
  4. GW13-15:DN, GW15-17:DN;
    No genes
  5. GW13-15:UP, GW15-17:not DE;
    id name description
    ENSG00000149054 ZNF215 zinc_finger_protein_215_[Source:HGNC_Symbol;Acc:13007]
    ENSG00000215845 TSTD1 thiosulfate_sulfurtransferase_(rhodanese)-like_domain_containing_1_[Source:HGNC_Symbol;Acc:35410]
    ENSG00000100336 APOL4 apolipoprotein_L,4[Source:HGNC_Symbol;Acc:14867]
    ENSG00000163823 CCR1 chemokine_(C-C_motif)receptor1_[Source:HGNC_Symbol;Acc:1602]
    ENSG00000169220 RGS14 regulator_of_G-protein_signaling_14_[Source:HGNC_Symbol;Acc:9996]
    ENSG00000203804 C1orf138 chromosome_1_open_reading_frame_138_[Source:HGNC_Symbol;Acc:32041]
    ENSG00000204520 MICA MHC_class_I_polypeptide-related_sequence_A_[Source:HGNC_Symbol;Acc:7090]
    ENSG00000080573 COL5A3 collagen,typeV,alpha3_[Source:HGNC_Symbol;Acc:14864]
    ENSG00000165379 LRFN5 leucine_rich_repeat_and_fibronectin_type_III_domain_containing_5_[Source:HGNC_Symbol;Acc:20360]
    ENSG00000213402 PTPRCAP protein_tyrosine_phosphatase,receptortype,C-associatedprotein_[Source:HGNC_Symbol;Acc:9667]
    ENSG00000139155 SLCO1C1 solute_carrier_organic_anion_transporter_family,member1C1_[Source:HGNC_Symbol;Acc:13819]
    ENSG00000187773 FAM69C family_with_sequence_similarity_69,memberC_[Source:HGNC_Symbol;Acc:31729]
    ENSG00000133216 EPHB2 EPH_receptor_B2_[Source:HGNC_Symbol;Acc:3393]
    ENSG00000119737 GPR75 G_protein-coupled_receptor_75_[Source:HGNC_Symbol;Acc:4526]
    ENSG00000126790 C14orf149 chromosome_14_open_reading_frame_149_[Source:HGNC_Symbol;Acc:20488]
    ENSG00000162733 DDR2 discoidin_domain_receptor_tyrosine_kinase_2_[Source:HGNC_Symbol;Acc:2731]
    ENSG00000108231 LGI1 leucine-rich,gliomainactivated_1_[Source:HGNC_Symbol;Acc:6572]
    ENSG00000161921 CXCL16 chemokine_(C-X-C_motif)ligand16_[Source:HGNC_Symbol;Acc:16642]
    ENSG00000119673 ACOT2 acyl-CoA_thioesterase_2_[Source:HGNC_Symbol;Acc:18431]
    ENSG00000135046 ANXA1 annexin_A1_[Source:HGNC_Symbol;Acc:533]
    ENSG00000215790 SLC35E2 solute_carrier_family_35,memberE2_[Source:HGNC_Symbol;Acc:20863]
    ENSG00000157150 TIMP4 TIMP_metallopeptidase_inhibitor_4_[Source:HGNC_Symbol;Acc:11823]
    ENSG00000170579 DLGAP1 discs,large(Drosophila)homolog-associatedprotein_1_[Source:HGNC_Symbol;Acc:2905]
    ENSG00000143252 SDHC succinate_dehydrogenase_complex,subunitC,integralmembrane_protein,15kDa[Source:HGNC_Symbol;Acc:10682]
    ENSG00000107796 ACTA2 actin,alpha2,smoothmuscle,aorta[Source:HGNC_Symbol;Acc:130]
    ENSG00000124193 SRSF6 serine/arginine-rich_splicing_factor_6_[Source:HGNC_Symbol;Acc:10788]
    ENSG00000152661 GJA1 gap_junction_protein,alpha1,43kDa[Source:HGNC_Symbol;Acc:4274]
    ENSG00000184110 EIF3C eukaryotic_translation_initiation_factor_3,subunitC_[Source:HGNC_Symbol;Acc:3279]
  6. GW13-15:DN, GW15-17:not DE;
    id name description
    ENSG00000166923 GREM1 gremlin_1_[Source:HGNC_Symbol;Acc:2001]
    ENSG00000164123 C4orf45 chromosome_4_open_reading_frame_45_[Source:HGNC_Symbol;Acc:26342]
    ENSG00000008196 TFAP2B transcription_factor_AP-2_beta_(activating_enhancer_binding_protein_2_beta)_[Source:HGNC_Symbol;Acc:11743]
    ENSG00000186897 C1QL4 complement_component_1,qsubcomponent-like_4_[Source:HGNC_Symbol;Acc:31416]
    ENSG00000054598 FOXC1 forkhead_box_C1_[Source:HGNC_Symbol;Acc:3800]
    ENSG00000104808 DHDH dihydrodiol_dehydrogenase_(dimeric)_[Source:HGNC_Symbol;Acc:17887]
    ENSG00000124813 RUNX2 runt-related_transcription_factor_2_[Source:HGNC_Symbol;Acc:10472]
    ENSG00000173068 BNC2 basonuclin_2_[Source:HGNC_Symbol;Acc:30988]
    ENSG00000165929 TC2N tandem_C2_domains,nuclear[Source:HGNC_Symbol;Acc:19859]
    ENSG00000157064 NMNAT2 nicotinamide_nucleotide_adenylyltransferase_2_[Source:HGNC_Symbol;Acc:16789]
    ENSG00000243244 STON1 stonin_1_[Source:HGNC_Symbol;Acc:17003]
    ENSG00000173809 TDRD12 tudor_domain_containing_12_[Source:HGNC_Symbol;Acc:25044]
    ENSG00000135333 EPHA7 EPH_receptor_A7_[Source:HGNC_Symbol;Acc:3390]
    ENSG00000231421
    ENSG00000168675 C18orf1 chromosome_18_open_reading_frame_1_[Source:HGNC_Symbol;Acc:1224]
    ENSG00000156395 SORCS3 sortilin-related_VPS10_domain_containing_receptor_3_[Source:HGNC_Symbol;Acc:16699]
    ENSG00000204103 MAFB v-maf_musculoaponeurotic_fibrosarcoma_oncogene_homolog_B_(avian)_[Source:HGNC_Symbol;Acc:6408]
    ENSG00000168447 SCNN1B sodium_channel,nonvoltage-gated1,beta[Source:HGNC_Symbol;Acc:10600]
    ENSG00000106546 AHR aryl_hydrocarbon_receptor_[Source:HGNC_Symbol;Acc:348]
    ENSG00000117598 NA Lipid_phosphate_phosphatase-related_protein_type_5_[Source:UniProtKB/Swiss-Prot;Acc:Q32ZL2]
    ENSG00000120322 PCDHB8 protocadherin_beta_8_[Source:HGNC_Symbol;Acc:8693]
    ENSG00000250305 NA Putative_methyltransferase_KIAA1456_[Source:UniProtKB/Swiss-Prot;Acc:Q9P272]
    ENSG00000106868 SUSD1 sushi_domain_containing_1_[Source:HGNC_Symbol;Acc:25413]
    ENSG00000183943 PRKX protein_kinase,X-linked[Source:HGNC_Symbol;Acc:9441]
    ENSG00000204060 FOXO6 forkhead_box_O6_[Source:HGNC_Symbol;Acc:24814]
    ENSG00000170941 NA Uncharacterized_protein_KIAA1456_[Source:UniProtKB/Swiss-Prot;Acc:Q8N9K7]
    ENSG00000063438 AHRR aryl-hydrocarbon_receptor_repressor_[Source:HGNC_Symbol;Acc:346]
    ENSG00000107902 LHPP phospholysine_phosphohistidine_inorganic_pyrophosphate_phosphatase_[Source:HGNC_Symbol;Acc:30042]
    ENSG00000169436 COL22A1 collagen,typeXXII,alpha1_[Source:HGNC_Symbol;Acc:22989]
    ENSG00000184985 SORCS2 sortilin-related_VPS10_domain_containing_receptor_2_[Source:HGNC_Symbol;Acc:16698]
    ENSG00000163328 GPR155 G_protein-coupled_receptor_155_[Source:HGNC_Symbol;Acc:22951]
    ENSG00000173598 NUDT4 nudix_(nucleoside_diphosphate_linked_moiety_X)-type_motif_4_[Source:HGNC_Symbol;Acc:8051]
    ENSG00000114200 BCHE butyrylcholinesterase_[Source:HGNC_Symbol;Acc:983]
    ENSG00000183722 LHFP lipoma_HMGIC_fusion_partner_[Source:HGNC_Symbol;Acc:6586]
    ENSG00000139722 VPS37B vacuolar_protein_sorting_37_homolog_B_(S.cerevisiae)[Source:HGNC_Symbol;Acc:25754]
  7. GW13-15:not DE, GW15-17:UP;
    id name description
    ENSG00000145247 OCIAD2 OCIA_domain_containing_2_[Source:HGNC_Symbol;Acc:28685]
    ENSG00000070748 CHAT choline_O-acetyltransferase_[Source:HGNC_Symbol;Acc:1912]
    ENSG00000165659 DACH1 dachshund_homolog_1_(Drosophila)_[Source:HGNC_Symbol;Acc:2663]
    ENSG00000165983 PTER phosphotriesterase_related_[Source:HGNC_Symbol;Acc:9590]
    ENSG00000139220 PPFIA2 protein_tyrosine_phosphatase,receptortype,fpolypeptide_(PTPRF),interactingprotein_(liprin),alpha2_[Source:HGNC_Symbol;Acc:9246]
    ENSG00000147255 IGSF1 immunoglobulin_superfamily,member1_[Source:HGNC_Symbol;Acc:5948]
    ENSG00000146233 CYP39A1 cytochrome_P450,family39,subfamilyA,polypeptide1_[Source:HGNC_Symbol;Acc:17449]
    ENSG00000181649 PHLDA2 pleckstrin_homology-like_domain,familyA,member2_[Source:HGNC_Symbol;Acc:12385]
    ENSG00000204516 MICB MHC_class_I_polypeptide-related_sequence_B_[Source:HGNC_Symbol;Acc:7091]
    ENSG00000164692 COL1A2 collagen,typeI,alpha2_[Source:HGNC_Symbol;Acc:2198]
    ENSG00000114805 PLCH1 phospholipase_C,eta1_[Source:HGNC_Symbol;Acc:29185]
    ENSG00000051523 CYBA cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577]
    ENSG00000145703 IQGAP2 IQ_motif_containing_GTPase_activating_protein_2_[Source:HGNC_Symbol;Acc:6111]
    ENSG00000165072 MAMDC2 MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673]
    ENSG00000130558 OLFM1 olfactomedin_1_[Source:HGNC_Symbol;Acc:17187]
    ENSG00000120318 ARAP3 ArfGAP_with_RhoGAP_domain,ankyrinrepeat_and_PH_domain_3_[Source:HGNC_Symbol;Acc:24097]
    ENSG00000198750 GATSL2 GATS_protein-like_2_[Source:HGNC_Symbol;Acc:37073]
    ENSG00000162849 KIF26B kinesin_family_member_26B_[Source:HGNC_Symbol;Acc:25484]
    ENSG00000134333 LDHA lactate_dehydrogenase_A_[Source:HGNC_Symbol;Acc:6535]
    ENSG00000064666 CNN2 calponin_2_[Source:HGNC_Symbol;Acc:2156]
  8. GW13-15:not DE, GW15-17:DN;
    id name description
    ENSG00000259210
    ENSG00000198650 TAT tyrosine_aminotransferase_[Source:HGNC_Symbol;Acc:11573]
    ENSG00000163053 SLC16A14 solute_carrier_family_16,member14_(monocarboxylic_acid_transporter_14)_[Source:HGNC_Symbol;Acc:26417]
    ENSG00000125637 PSD4 pleckstrin_and_Sec7_domain_containing_4_[Source:HGNC_Symbol;Acc:19096]
    ENSG00000153822 KCNJ16 potassium_inwardly-rectifying_channel,subfamilyJ,member16_[Source:HGNC_Symbol;Acc:6262]
    ENSG00000188803 SHISA6 shisa_homolog_6_(Xenopus_laevis)_[Source:HGNC_Symbol;Acc:34491]
    ENSG00000127952 STYXL1 serine/threonine/tyrosine_interacting-like_1_[Source:HGNC_Symbol;Acc:18165]
    ENSG00000150907 FOXO1 forkhead_box_O1_[Source:HGNC_Symbol;Acc:3819]
    ENSG00000076344 RGS11 regulator_of_G-protein_signaling_11_[Source:HGNC_Symbol;Acc:9993]
    ENSG00000174938 SEZ6L2 seizure_related_6_homolog_(mouse)-like_2_[Source:HGNC_Symbol;Acc:30844]
    ENSG00000122694 GLIPR2 GLI_pathogenesis-related_2_[Source:HGNC_Symbol;Acc:18007]
    ENSG00000167774 NDUFA7 NADH_dehydrogenase_(ubiquinone)1alpha_subcomplex,7,14.5kDa_[Source:HGNC_Symbol;Acc:7691]
    ENSG00000132164 SLC6A11 solute_carrier_family_6_(neurotransmitter_transporter,GABA),member_11_[Source:HGNC_Symbol;Acc:11044]

DAVID enrichment for DE genes

  • GW associated DE genes shared by cell types show no enrichment due to small gene lists.
  • GW15 vs GW 13: calcium ion binding in cortex UP and GE DN, neurogenesis in cortex DN.
  • GW17 vs GW 15: neurogenesis in GE, no enrichment in cortex.
  • GW17 vs GW 13: calcium ion binding in cortex UP and GE UP, neurogenesis in GE DN.

Isoform analysis

Sample DE_genes DE_exons with_expressed_genes isoform_exons exclude_DE_genes isoform_genes GW
Cortex-HuFNSC01_Cortex-HuFNSC03 565 28637 16045 8044 7772 2490 17 vs 15
Cortex-HuFNSC01_Cortex-HuFNSC04 530 27428 13200 6365 6134 2167 17 vs 13
Cortex-HuFNSC02_Cortex-HuFNSC03 681 28963 16765 7961 7630 2425 17 vs 15
Cortex-HuFNSC02_Cortex-HuFNSC04 722 29416 13894 6351 6011 2105 17 vs 13
Cortex-HuFNSC03_Cortex-HuFNSC04 642 26826 12185 5818 5479 1994 15 vs 13
GE-HuFNSC01_GE-HuFNSC03 861 31361 14725 5880 5458 2041 17 vs 15
GE-HuFNSC01_GE-HuFNSC04 883 34359 15889 6401 5996 2049 17 vs 13
GE-HuFNSC02_GE-HuFNSC03 921 32827 15557 5773 5306 1965 17 vs 15
GE-HuFNSC02_GE-HuFNSC04 869 34699 16012 6113 5711 1986 17 vs 13
GE-HuFNSC03_GE-HuFNSC04 545 24752 12223 4582 4422 1454 15 vs 13